Source code for ClearMap.Utils.path_utils
"""
Utility functions for working with paths
"""
import os
from pathlib import Path
from ClearMap.config.config_loader import ConfigLoader
[docs]
def is_feather(f):
"""
Check if a file is a feather file
.. warning::
Currently, this function only checks if the file ends with 'cells.feather'
Parameters
----------
f : str or Path
The file to check
Returns
-------
"""
if isinstance(f, Path):
f = str(f)
return f.endswith('cells.feather') # FIXME: check does not match name
[docs]
def is_density_file(f_name):
f_name = os.path.basename(f_name)
if 'debug' in f_name:
return False
# return 'density' in f_name and f_name.endswith('.tif')
return f_name.endswith('density_counts.tif') # FIXME add menu for alternatives
[docs]
def find_density_file(target_dir):
return find_file(target_dir, is_density_file, 'density')
[docs]
def find_cells_df(target_dir):
"""
Find the first feather file in ``target_dir``
Parameters
----------
target_dir
Returns
-------
"""
return find_file(target_dir, is_feather, 'feather')
[docs]
def find_file(target_dir, check_func, file_type_name):
"""
Find the first file corresponding to ``check_func`` in ``target_dir``
Parameters
----------
target_dir : str
The directory to search
check_func : callable
A function that takes a file name and returns a boolean
file_type_name : str
The name of the file type to search for. This is used for error messages
Returns
-------
"""
files = [os.path.join(target_dir, f) for f in os.listdir(target_dir) if check_func(f)]
try:
return files[0]
except IndexError:
raise RuntimeError(f'No {file_type_name} file found in {target_dir}')
[docs]
def dir_to_sample_id(folder):
"""
Get the sample ID from a directory
Parameters
----------
folder : str
The directory to check
Returns
-------
"""
cfg_loader = ConfigLoader(folder)
return cfg_loader.get_cfg('sample')['sample_id']
